6.22. XYZ trajectory reader — MDAnalysis.coordinates.XYZ

The XYZ format is a loosely defined, simple coordinate trajectory format. The implemented format definition was taken from the VMD xyzplugin and is therefore compatible with VMD.

Note the following:

  • Comments are not allowed in the XYZ file (we neither read nor write them to remain compatible with VMD).
  • The atom name (first column) is ignored during reading.
  • The coordinates are assumed to be space-delimited rather than fixed width (this may cause issues - see below).
  • All fields to the right of the z-coordinate are ignored.
  • The unitcell information is all zeros since this is not recorded in the XYZ format.

Units

  • Coordinates are in Angstroms.
  • The length of a timestep can be set by passing the dt argument, it’s assumed to be in ps (default: 1 ps).

There appears to be no rigid format definition so it is likely users will need to tweak this class.

6.22.1. XYZ File format

Definition used by the XYZReader and XYZWriter (and the VMD xyzplugin from whence the definition was taken):

[ comment line            ] !! NOT IMPLEMENTED !! DO NOT INCLUDE
[ N                       ] # of atoms, required by this xyz reader plugin  line 1
[ molecule name           ] name of molecule (can be blank)                 line 2
atom1 x y z [optional data] atom name followed by xyz coords                line 3
atom2 x y z [ ...         ] and (optionally) other data.
...
atomN x y z [ ...         ]                                                 line N+2

Note

  • comment lines not implemented (do not include them)
  • molecule name: the line is required but the content is ignored at the moment
  • optional data (after the coordinates) are presently ignored

6.22.2. Classes

class MDAnalysis.coordinates.XYZ.XYZReader(filename, **kwargs)[source]

Reads from an XYZ file

Data:
ts

Timestep object containing coordinates of current frame
Methods:
len(xyz)

return number of frames in xyz

for ts in xyz:

iterate through trajectory

The XYZ file format follows VMD’s xyzplugin and is also described under XYZ format.

Changed in version 0.11.0: Frames now 0-based instead of 1-based. Added dt and time_offset keywords (passed to Timestep)

Writer(filename, n_atoms=None, **kwargs)[source]

Returns a XYZWriter for filename with the same parameters as this XYZ.

Parameters:
  • filename (str) – filename of the output trajectory
  • n_atoms (int (optional)) – number of atoms. If none is given use the same number of atoms from the reader instance is used
  • **kwargs – See XYZWriter for additional kwargs
Returns:
Return type:

XYZWriter (see there for more details)

See also

XYZWriter

close()[source]

Close xyz trajectory file if it was open.

n_atoms

number of atoms in a frame

class MDAnalysis.coordinates.XYZ.XYZWriter(filename, n_atoms=None, atoms=None, convert_units=True, remark=None, **kwargs)[source]

Writes an XYZ file

The XYZ file format is not formally defined. This writer follows the VMD implementation for the molfile xyzplugin.

Initialize the XYZ trajectory writer

Parameters:
  • filename (str) – filename of trajectory file. If it ends with “gz” then the file will be gzip-compressed; if it ends with “bz2” it will be bzip2 compressed.
  • n_atoms (int (optional)) – Number of atoms in trajectory. By default assume that this is None and that this file is used to store several different models instead of a single trajectory. If a number is provided each written TimeStep has to contain the same number of atoms.
  • atoms (str | list (optional)) – Provide atom names: This can be a list of names or an AtomGroup. If none is provided, atoms will be called ‘X’ in the output. These atom names will be used when a trajectory is written from raw Timestep objects which do not contain atom information. If you write a AtomGroup with XYZWriter.write() then atom information is taken at each step and atoms is ignored.
  • convert_units (bool (optional)) – convert quantities to default MDAnalysis units of Angstrom upon writing [True]
  • remark (str (optional)) – single line of text (“molecule name”). By default writes MDAnalysis version and frame
  • versionchanged: (.) – 1.0.0: Removed default_remark variable (Issue #2692).
close()[source]

Close the trajectory file and finalize the writing

write(obj)[source]

Write object obj at current trajectory frame to file.

Atom elements (or names) in the output are taken from the obj or default to the value of the atoms keyword supplied to the XYZWriter constructor.

Parameters:obj (Universe or AtomGroup) – The AtomGroup or Universe to write.

Deprecated since version 1.0.0: Deprecated the use of Timestep as arguments to write. Use either an AtomGroup or Universe. To be removed in version 2.0.